tbuckley/cabot-search huggingface dataset:
Abstract 1934: An artificial intelligence-based framework for BLEACH&amp;STAIN mfIHC facilitates automated prognosis marker assessment in breast cancer
Authors: Tim Mandelkow, Elena Bady, Magalie C. Lurati, Claudia Hube-Magg, Maximilian Lennartz, Guido Sauter, Niclas C. Blessin, Ronald Simon
Journal: Cancer Research (2022)

Abstract The assessment of prognostic markers in routine clinical practice of breast cancer is currently performed using multi gene RNA panels. However, the unknown proportion of normal breast tissue in relation to malignant breast tissue can reduce the predictive value of such tests. Immunohistochemistry holds the potential for a better assessment of tumors because tumor cells can be separately analyzed. To enable automated prognosis marker detection (i.e. HER2, GATA3, progesterone receptor [PR], estrogen receptor [ER], androgen receptor [AR], TOP2A, Ki-67, TROP2, Mammaglobin), we have developed and validated a framework for automated breast cancer identification, which comprises three different artificial intelligence analysis steps and an algorithm for cell-distance analysis of 12+1 marker BLEACH&amp;STAIN multiplex fluorescence immunohistochemistry staining, in 2004 breast cancers. The optimal distance between Myosin+ basal cells and benign panCK+ benign cells was identified as 31µm and used to exclude benign glands from the analysis combined with and deep learning-based algorithm for benign gland detection. Our deep learning-based framework discriminated normal glands from malignant glands with an area under receiver-operating characteristic curves (AUC) of 0.96 (95% confidence interval [CI], 0.92 to 0.99). The accuracy of the approach was also validated by several well-characterized biological findings, such as the identification of 13% HER2+, 73% PR+/ER+, and 14% triple negative cases in the study cohort as well as a significant higher Fraction of TOP2A in the HER2+ cases as compared to the HER2- cases (p&amp;lt;0.001). Furthermore, the automated assessment of GATA3, PR, ER, TOP2A-LI, Ki-67-LI, TROP2, and Mammaglobin was significantly liked to the tumor grade (p&amp;lt;0.001 each). Furthermore, a high expression level of HER2, GATA3, PR, and ER was associated with a prolonged overall survival (p≥0.002 each). In conclusion, a deep learning-based framework for automated breast cancer identification using BLEACH&amp;STAIN multiplex fluorescence IHC facilitates automated prognosis marker quantification in breast cancer. Citation Format: Tim Mandelkow, Elena Bady, Magalie C. Lurati, Claudia Hube-Magg, Maximilian Lennartz, Guido Sauter, Niclas C. Blessin, Ronald Simon. An artificial intelligence-based framework for BLEACH&amp;STAIN mfIHC facilitates automated prognosis marker assessment in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1934.
Human macrophage polarization determines bacterial persistence of Staphylococcus aureus in a liver-on-chip-based infection model
Authors: Fatina Siwczak, Zoltan Cseresnyes, Mohamed I.Abdelwahab Hassan, Kehinde Oluwasegun Aina, Swen Carlstedt, Anke Sigmund, Marko Groger, Bas G.J. Surewaard, Oliver Werz, Marc Thilo Figge, Lorena Tuchscherr, Bettina Loffler, Alexander S. Mosig
Journal: Biomaterials (2022)

Infections with Staphylococcus aureus (S. aureus) have been reported from various organs ranging from asymptomatic colonization to severe infections and sepsis. Although considered an extracellular pathogen, S. aureus can invade and persist in professional phagocytes such as monocytes and macrophages. Its capability to persist and manipulate macrophages is considered a critical step to evade host antimicrobial reactions. We leveraged a recently established human liver-on-chip model to demonstrate that S. aureus specifically targets macrophages as essential niche facilitating bacterial persistence and phenotype switching to small colony variants (SCVs). In vitro, M2 polarization was found to favor SCV-formation and was associated with increased intracellular bacterial loads in macrophages, increased cell death, and impaired recruitment of circulating monocytes to sites of infection. These findings expand the knowledge about macrophage activation in the liver and its impact on bacterial persistence and dissemination in the course of infection.
Abstract 406: Mechanism of AXL regulation in chemotherapy resistance
Authors: Mehreen Ahmed, Julhash Uddin Kazi
Journal: Cancer Research (2022)

Abstract Constitutive activation of receptor tyrosine kinase AXL is an important phenomenon in chemotherapy resistance and is highly expressed in several malignancies. Although studies over the past decade revealed that AXL is upregulated during treatment, the biological significance and the mechanism by which AXL is activated upon chemotherapy are yet to be determined. In this study, we aim to understand the biology of AXL mediated chemo-resistance, and the consequences of AXL activation. To investigate the biological significance of AXL, we generated iRFP-luciferase-expressing cell lines which facilitate live monitoring of cancer progression during treatment in an in vivo setting. In parallel, by knocking down AXL using shRNA, we observed inhibitory effect on cell migration and tumor forming efficiency in vitro. Moreover, using in vitro cell based models, we showed that while AXL expression was upregulated upon treatment with chemotherapeutic agents, pharmacological inhibition of AXL caused synergistic effect between selective AXL inhibitors and cisplatin. Additionally, our data suggest that upregulation of AXL and its tyrosine phosphorylation may mediate resistance to chemotherapy. Using phosphoproteomics, we identified a link between CDK9 activation and drug-induced AXL expression. We showed that while AXL expression was upregulated upon treatment with tyrosine kinase inhibitor, pharmacological inhibition of CDK9 completely blocked AXL expression. Collectively, our data suggest that activation of kinase signaling might be required for AXL repression, and thereby, for targeting AXL-axis in chemotherapy resistance. Citation Format: Mehreen Ahmed, Julhash Uddin Kazi. Mechanism of AXL regulation in chemotherapy resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 406.
Abstract 1364: Spatially resolved T-cell receptor profiling elucidates relationships between TCR diversity, immune infiltration, and cancer-associated pathways
Authors: Michelle A. Kriner, Katrina van Raay, Jason W. Reeves, Kit A. Fuhrman, Andrew Klock, Alecksandr Kutchma, Erin Piazza, Joseph Beechem
Journal: Cancer Research (2022)

Abstract As T-cells mature, genes encoding T-cell receptor (TCR) segments are somatically recombined to generate a diverse repertoire of receptors specific to unique antigens. The resultant TCR diversity, and subsequent clonal expansion events, are critical in understanding the adaptive immune response to pathogens and cancers. While many methods have been developed to determine specific clonotypes and overall TCR diversity present in various tissues, these methods to date have failed to capture spatial orientation and arrangement of T-cells engaging with their microenvironment. Tracking T-cell migration and infiltration into the tumor has thus been limited to post-hoc low-plex profiling methods. To better understand T-cell localization during tumor development, we have developed a TCR profiling panel for the GeoMx® Digital Spatial Profiler that can be combined with the GeoMx Cancer Transcriptome Atlas (CTA) or Human Whole Transcriptome Atlas (WTA). This novel spatial assay enables simultaneous quantification of all functional TCR constant, variable and joining segments in situ along with transcriptome-wide gene expression profiling in spatially defined regions of a tissue. We validated the performance of the TCR probe pool in inflamed tonsil and cell pellet arrays, demonstrating comparable sensitivity and specificity relative to orthogonal methods. We next used the GeoMx TCR spike-in panel to characterize intra- and inter-patient TCR heterogeneity in a cohort of 68 T-cell lymphomas to track clonal interactions between the malignant and non-malignant immune microenvironment. We demonstrate the ability to link the spatial context of TCR segment expression to activation of malignant signaling cascades as well as non-cancerous T-cell response to the presence of other immune cells and cancer-associated signaling. Together, the combination of our TCR spike-in panel with the CTA or WTA illuminates spatial distribution of T-cell clones paving the way for studies to comprehensively link TCR clonality changes to the tumor microenvironment. FOR RESEARCH USE ONLY. Not for use in diagnostic procedures. Citation Format: Michelle A. Kriner, Katrina van Raay, Jason W. Reeves, Kit A. Fuhrman, Andrew Klock, Alecksandr Kutchma, Erin Piazza, Joseph Beechem. Spatially resolved T-cell receptor profiling elucidates relationships between TCR diversity, immune infiltration, and cancer-associated pathways [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1364.
Abstract 152: Discovery and characterization of GSK3 allosteric activators
Authors: Reeba P. Varghese, Curtis A. Thorne
Journal: Cancer Research (2022)

Abstract The intestinal epithelium undergoes constant regeneration and is tightly regulated. Disruption of its homeostasis can result in the development of colorectal cancer (CRC). Glycogen synthase kinase 3 (GSK3) is a kinase that plays a central role in multiple signaling pathways, including cellular proliferation, where it inhibits the activity of its substrates. GSK3 dynamics can be described as a multiple input multiple output system. Numerous upstream growth factors can regulate and thus inhibit GSK3 from acting on its many substrates. Mutations in these growth signaling pathways (e.g., Wnt and KRAS) have been well established to have a role in CRC progression. Therefore, aberrantly activated signaling due to these proteins are presumed to result in the constitutive inhibition of GSK3 activity in CRC, thus making it an ideal therapeutic target. The aim of this study is to discover an allosteric GSK3 small molecule activator that can restore GSK3 kinase activity within CRC. Method: We screened 50,000 small molecule compounds using a luciferase-based in-vitro kinase assay. We are further confirming our top hits using both chemical and cell-based assays. For the cell-based assays, we test the compounds in human colonic epithelial cells (HCEC) and its three isogenic cell lines, which mimic CRC progression, and monitor changes in GSK3 kinase activity indirectly, via changes in its substrate protein levels, and directly via a live-cell GSK3 specific reporter. In addition, the top hits are also tested in both normal colon and CRC organoids. Results: Prior to running our large screen, we performed various optimization steps to determine the ideal condition for our screening assay. Our screening assay scored a Z-Score of 0.5 and higher, which indicated that it was a high-quality screening assay. Additionally, we have developed two cell-based orthogonal HTS assays. One using immunofluorescence and single-cell quantification of 24 GSK3 substrates from various pathways in our cell lines. Second, we engineered a GSK3 live-cell reporter and expressed it in the HCEC cells and three isogenic cell lines and organoid models. Impact: There is a need for advancements in preventative or therapeutic targets against CRC. Research indicates that suppression of GSK3 enzymatic activity decreases sensitivity to certain chemotherapeutic and targeted therapies. Therefore, restoring GSK3 enzymatic activity in CRC may re-sensitize tumors to other targeted therapies and establish GSK3 as a potential therapeutic target. Citation Format: Reeba P. Varghese, Curtis A. Thorne. Discovery and characterization of GSK3 allosteric activators [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 152.
Abstract 5401: Fluoxetine inhibit osteosarcoma progression via RANK/RANKL signaling pathway
Authors: Peggy Tan, Fei-Ting Hsu, I-Tsang Chiang, Yuan Chang
Journal: Cancer Research (2022)

Abstract Osteosarcoma (OS) is an aggressive malignant bone cancer commonly occurs on adolescent. OS was mostly found at sites of bone growth. Sixty percent OS cases happen at knee, 15% around hip, 10% shoulder and 8% jaw. Non-stop osteoclast cells differentiation by which osteoblasts secrete RANKL bind to RANK receptor on osteoclasts’ cell surface, stimulate rapid bone metabolism and considerable as an important signaling pathway correlate with OS progression. Depressant is usually occurring in cancer patients. Several reports suggested that several anti-depressant drugs presented anti-tumour potential. Previous study has reported, fluoxetine, a prescription antidepressant can inactivate NF-κB and thus suppress hepatocellular carcinoma and non-small cell lung cancer progression. Furthermore, fluoxetine may inhibit DNA repair in non-small cell lung cancer. In our study, the MTT assay demonstrated fluoxetine significantly reduced viability of U-2 OS cells. Next, target protein RANK/RANKL expression were also downregulated by fluoxetine in dose dependent manner. Besides, STAT3 mediated NF-κB activity, were also inactivated by fluoxetine. Additionally, the expression of PARP1 (DNA damage related, and several oncogenes such as XIAP and Cyclin D1 were also downregulated by fluoxetine in dose dependent manner. Moreover, the inhibition of tumour angiogenesis by fluoxetine has also proven by using aorta ring assay. Further in vivo experiment may need to be performed to identify anti-tumor efficacy of fluoxetine. In sum, fluoxetine can be used anti-tumour adjuvant of OS therapy and the detailed mechanism or further combination strategy may be worth exploring. Citation Format: Peggy Tan, Fei-Ting Hsu, I-Tsang Chiang, Yuan Chang. Fluoxetine inhibit osteosarcoma progression via RANK/RANKL signaling pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5401.
Abstract 2307: Sequential treatment with abemaciclib plus endocrine therapy inhibits cell proliferation and triggers apoptosis in cell lines resistant to CDK4/6i
Authors: Elisabet Zapatero-Solana, Maria P. Ganado, Maria J. Ortiz-Ruiz, Cecilia Mur, Lacey Litchfield, Farhana Merzoug, Oscar Puig, Maria Jsoe Lallena
Journal: Cancer Research (2022)

Abstract CDK4/6 inhibitors combined with endocrine therapy (ET) have shown clinical benefit in HR+, HER2- breast cancer. However, development of resistance highlights the need for treatment strategies to improve outcomes. To study resistance mechanisms, breast cancer cell lines were treated with CDK4/6i (abemaciclib or palbociclib) in combination with 4-OH-tamoxifen (tamoxifen) for 120-144h and sorted for resistant cells defined as geminin positive (GEM+), a marker of S/G2/M cell cycle accumulation. To confirm the resistant phenotype, cell lines were treated with tamoxifen plus the CDK4/6 inhibitor used to drive resistance. To understand if sequential CDK4/6i treatment is effective in controlling cell proliferation, resistant cells generated through treatment with palbociclib + tamoxifen or abemaciclib + tamoxifen were treated with abemaciclib + ET (fulvestrant or tamoxifen) or palbociclib + ET, respectively. Geminin/Ki67, annexin V and colony formation assays were performed to evaluate cell proliferation and viability. Molecular characterization by western blot and RNAseq analysis were utilized to provide insights into mechanisms of resistance and the effects of sequential treatment with CDK4/6i + ET. Cell lines resistant to palbociclib + tamoxifen subsequently treated with abemaciclib + ET showed decreased %GEM+ and colony formation ability, decreased Ki67 levels, and increased apoptosis. These effects were not observed in cell lines resistant to abemaciclib + tamoxifen following subsequent treatment with palbociclib + ET. Western blot analysis showed that palbociclib and abemaciclib-resistant cells had increased CDK6 and pERK levels, compared to control. Importantly, treatment of palbociclib-resistant cells with abemaciclib + ET decreased FOXM1, a key regulator of senescence and apoptosis. Cyclin A, a marker of mitosis, was also decreased, consistent with decreased %GEM+ subpopulation in palbociclib + ET resistant cells. These effects were not observed in abemaciclib-resistant cells treated with palbociclib + ET.In summary, our in vitro data provides mechanistic insights into resistance to combination CDK4/6i + tamoxifen and suggests the potential benefit of sequential treatment with abemaciclib + ET to overcome resistance in breast cancer. Citation Format: Elisabet Zapatero-Solana, Maria P. Ganado, Maria J. Ortiz-Ruiz, Cecilia Mur, Lacey Litchfield, Farhana Merzoug, Oscar Puig, Maria Jsoe Lallena. Sequential treatment with abemaciclib plus endocrine therapy inhibits cell proliferation and triggers apoptosis in cell lines resistant to CDK4/6i [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2307.
Abstract 5144: Using proteomic approach to identify potential tumor-associated antigens (TAAs) as biomarkers in Hispanic hepatocellular carcinoma
Authors: Yangcheng Ma, Cuipeng Qiu, Xiaojun Zhang, Xiao Wang, Jianying Zhang
Journal: Cancer Research (2022)

Abstract Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide with high prevalence and poor prognosis. The incidence rate and mortality rate in Hispanic HCC is relative higher than other ethnic groups. Autoantibodies against tumor associated antigens (TAAs) have long been proved as useful biomarkers in cancer diagnosis. In the present study, sera from 25 Hispanic patients with HCC and 25 sera from normal individuals were used in a proteomic approach to identify HCC-related TAAs. Twenty-four immunoreactive protein spots (16 from HepG2 cells, and 8 from SUN449 cells) were excised from the two-dimensional electrophoresis (2DE) gels, digested with trypsin, and subsequently analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Of 24 immunoreactive protein spots, 21 were identified with compatible molecular weights and isoelectric points. After further analysis, a total of 9 proteins were found to be potential TAAs, including endoplasmic reticulum chaperone BiP (HSPA5), 60 kDa heat shock protein (HSP60), triosephosphate isomerase (TPI1), protein disulfide-isomerase (PDI), Actin-cytoplasmic 2 (ACTG1), calreticulin (CRP55), alpha-enolase (ENO1), heat shock 70 kDa protein (HSP70), tropomyosin alpha-3 chain (TPM3). Among these proteins, HSPA5 was corresponded to 5 protein spots on the 2DE gels, while 4 proteins (HSPA5, HSP60, TPI1 and PDI) were found in both HepG2 and SNU449 cell lines. Enrichment analysis show that these proteins are mostly responsible for protein folding in endoplasmic reticulum as well as ubiquitin ligase binding function. In the subsequent study, autoantibodies against these proteins will be detected by immunoassay, and further evaluated as biomarkers in detection of Hispanic HCC. Citation Format: Yangcheng Ma, Cuipeng Qiu, Xiaojun Zhang, Xiao Wang, Jianying Zhang. Using proteomic approach to identify potential tumor-associated antigens (TAAs) as biomarkers in Hispanic hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5144.
Abstract 3841: SMIM11A, a novel protein involved in the mechanism of vasculogenic mimicry formation <i>in vitro</i>
Authors: Gabriel Mingo, Javiera Pradenas, Nicole Babbitt, Pamela González, Cristina Bertocchi, Gareth Owen
Journal: Cancer Research (2022)

Abstract Introduction: Vasculogenic mimicry (VM) describes a process by which cancer cells establish an alternative perfusion pathway in an endothelial cell-free manner. Despite the strong correlation with reduced patient survival, the mechanisms by which a tumor can create this self-generated irrigation system are still not fully understood. The process of VM in vitro can occur in laminin-111-containing Matrigel and requires the PI3K pathway. However, the membrane protein component and signaling pathways involved in this process are unknown. Methods: In an established in vitro model of VM of ovarian and breast cancer cells (HEY and MDA-MB-231, respectively) on Matrigel coating, we utilized gene silencing and blocking antibodies to elucidate the signaling pathways involved in this process. RNASeq was used to identify novel transcripts and siRNA was utilized to verify the requirement of candidate RNA/protein in tubular formation. Results: siRNA and antibody blocking of integrin β1, but not β3, prevented VM formation in vitro. Individual silencing of cortactin, TKS5, MMP-2, MMP-9 and MMP-14 affected tubular formation. RNAseq analysis suggested that VM has minimal dependence on de novo transcriptional activity yet reported a strong upregulation of small Integral Membrane Protein 11 (SMIM11A). This result was verified by qPCR and siRNA silencing of SMIM11A prevented VM formation. Discussion: Laminin 111 may interact with integrin β1, and the consequent activation of the PI3K pathway could potentially remodel cytoskeletal proteins and promote the activity of MMPs. We report for the first time a biological role for SMIM11a. This gene is regulated at the RNA level and is required for the formation of tubular structure in vitro. As VM is strongly associated with poor patient survival, understanding the formation of this alternative irrigation system may deliver new druggable targets. Citation Format: Gabriel Mingo, Javiera Pradenas, Nicole Babbitt, Pamela González, Cristina Bertocchi, Gareth Owen. SMIM11A, a novel protein involved in the mechanism of vasculogenic mimicry formation in vitro [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3841.